Thanks for alerting us to this problem. It will take me awhile to investigate the differences between what 1.7 is doing and what currently happens. I have opened a ticket in our issue-tracking database (#20506 (Modeller results worse)) so that you will receive notifications as progress occurs on resolving the problem.

On Jun 17, 2026, at 9:02 AM, Roberto Marabini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I am using the ChimeraX modeller comparative command in both ChimeraX
1.7 and ChimeraX 1.11.1. The command executes successfully in both
versions, but the results are significantly different. The model
generated with ChimeraX 1.7 appears correct, whereas the model
generated with ChimeraX 1.11.1 appears incorrect.

One notable difference is the GA341 "correlation" score: it is close
to 1.0 (high confidence) in ChimeraX 1.7, but close to 0.0 (very low
confidence) in ChimeraX 1.11.1.

The test data is:

Sequence: UniProt P69905 (human hemoglobin)
Template structure: PDB 2DHB (horse hemoglobin)
Alignment: attached file

The exact command used was generated using chimerax GUI:

modeller comparative aligned_1.fasta:2 numModels 5 fast false
multichain true hetPreserve false hydrogens false waterPreserve false

Has anyone observed similar differences between ChimeraX versions, or
can suggest a way to obtain consistent Modeller results in the latest
releases of ChimeraX?

Thanks in advance for any help.

Roberto
<aligned_1.fasta>_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/